What Smoldyn is

Smoldyn is a computer program for cell-scale biochemical simulations. It simulates each molecule of interest
individually to capture natural stochasticity and to yield nanometer-scale spatial resolution. It treats other
molecules implicitly, enabling it to simulate hundreds of thousands of molecules over several minutes of real time.
Simulated molecules
diffuse, react, are confined by surfaces, and bind to membranes much as they would in a real biological system.

Smoldyn is easy to use and easy to install. It is more accurate and faster than other particle-based
simulators. Smoldyn's unique features include: a "virtual experimenter" who can manipulate or measure the simulated
system, support for spatial compartments, molecules with excluded volume, and simulations in 1, 2, or 3 dimensions.

News

Smoldyn 2.52 released May 16, 2017

Partial support for moving surfaces

Compartments can translate or diffuse.

Rule-based modeling with wildcards or BioNetGen.

On-the-fly reaction network generation.

Rules for molecular properties

Properties for rule-based reactions

Improved arithmetic in input files.

Minor bug fixes.

Research Highlight

Meinecke, L. and M. Eriksson,
ArXiv 2016

Simulations with off-lattice Brownian dynamics (e.g. Smoldyn) are computationally expensive in
crowded environments. This paper investigates the extent to which on-lattice simulations can
simulate reactions and diffusion in the presence of crowders. The authors show that diffusion is
slowed down in the off-lattice model since randomly distributed obstacles effectively exclude more volume than those
ordered on an artificial grid. Crowded reaction rates can be both increased and decreased by the grid structure. Grid
artifacts increase with increasing crowder density. The authors conclude that the computationally more efficient on-lattice
simulations are accurate only for low crowder densities.

Smoldyn is written and maintained by Steve Andrews. Development has been
supported by the National Institutes of Health, the U.S. Department of Energy, the National Science
Foundation, and the MITRE Corporation, albeit never by funding that was dedicated specifically for this purpose.